Could it be that many of the above posts have part of it right and that there is no one answer?
In thinking about it myself (based on my own experiences) I really think it is a number of things.
1) People who are genuinely sympathetic to what they see as a CIS-gendered person who is presenting androgenously. They want the person to feel welcome, appreciated, and respected as a human being... they just don't realize that the person presenting before them *is* trans and that being mis-gendered hurts.
2) Societal expectations: You are either a man or a woman, period. Being called the wrong thing is very offensive. Most times, this gendering is an easy call, and it is a way to communicate and identify with someone in a manner far more personable and "socially correct". So, for most people, using a gender marker in what they say to someone is an important social lubricant.
In the case of trans* people, this can be a grave mistake, but we're not all that well known yet.
3) Too clever to be "fooled": Some people seem to feel like someone dressed in the other gender's clothing is out to fool them, making a joke at their expense. They like to show that they aren't "fooled" by addressing a trans* person presenting in their true gender as their bio gender. Their fragile egos cannot grasp that this person may *be* the other gender. Pro-tip: Getting offended can really fluster this type. They're expecting to be "in on the joke" and "on your side"... if they are corrected sternly they often sputter a bit and blush. Maybe it is helpful to do so... maybe not. I can imagine in certain situations this can be dangerous, especially if your trans* status were to become known to them.
Of the above, I like people who fall into category three the most. Once educated, they tend to be very understanding. Category 2 seems to fit the vast majority of the people I meet. Category 3 are the worst, I think, because they can be so touchy. I will correct a Category 1 if I have the opportunity, a Category 2 if it feels like it matters enough to me (rarely), but a Category 3 I try very hard to ignore.
That being said, I *was* rather proud once when I corrected a waiter. I was in a restaurant with my family (who used all female pronouns for me
and called me Robin in front of said waiter). The water hesitated before calling me "sir" the first time and I let it slide, thinking of him as a category 2-3... but afterward, when he brought the check, he called me "sir" with a smirk. Ah. A hesitant Category 3 mis-genderist. So, when he came to pick up my credit card, I held on to it, locked eyes with him, and said, "I understand that I appear to be fairly masculine. I am tall, I have a deep voice, and some of my features are not very feminine. I have some advice for you, though... if you find yourself serving someone in makeup, a wig, and cosmetics who is obviously presenting herself as a woman, treat her like a woman. I believe you will find they tip you much better if you do so." The waiter kind of blanched, then said, "I'm sorry... ma'am?" to which I replied, "Thank you. I hope you have a better day."
I haven't been back for a month, but I hope to find when I do return his treatment of me has improved. It would be a nice surprise.

*hug*
*edited because I got confused on my own numbers...